@weng-lab/ui-components 2.0.3 → 2.1.0

package/dist/ui-components.es11.js

@@ -1,100 +1,332 @@
-import { c as K } from "./ui-components.es13.js";
-import { useState as Q, useRef as T, useEffect as U } from "react";
-import { getGenes as X, getCCREs as Y, getLegacyCCREs as Z, getICREs as D, getSNPs as ee, getStudys as te } from "./ui-components.es56.js";
-import { isDomain as G, geneResultList as se, ccreResultList as re, getCoordinates as oe, legacyCcreResultList as ce, icreResultList as ne, snpResultList as ie, studyResultList as le, OmesList as ae, omeResultsList as ue } from "./ui-components.es55.js";
-function he(i, j) {
-  const e = K.c(36);
-  let w;
-  e[0] !== i ? (w = Array.isArray(i) ? i : [i], e[0] = i, e[1] = w) : w = e[1];
-  const d = w, {
-    queries: c,
-    assembly: n,
-    geneVersion: u,
-    limits: t,
-    showiCREFlag: m,
-    debounceMs: N
-  } = j, C = N === void 0 ? 200 : N, [A, W] = Q(null), [M, p] = Q(!1), [O, P] = Q(null), f = T(null), L = T(null);
-  let S;
-  e[2] !== n || e[3] !== C || e[4] !== u || e[5] !== d || e[6] !== t?.ccre || e[7] !== t?.gene || e[8] !== t?.icre || e[9] !== t?.legacyCcre || e[10] !== t?.ome || e[11] !== t?.snp || e[12] !== t?.study || e[13] !== c || e[14] !== m ? (S = () => {
-    f.current && (window.clearTimeout(f.current), f.current = null), L.current && (L.current.abort(), L.current = null);
-    const v = d.filter(fe);
-    if (v.length === 0) {
-      W([]), p(!1), P(null);
-      return;
+import { j as a } from "./ui-components.es13.js";
+import { isAutogeneratedRow as u, gridRowIdSelector as y, gridRowNodeSelector as p } from "@mui/x-data-grid-premium";
+import { AssayWheel as h } from "./ui-components.es9.js";
+import { DownloadButton as o } from "./ui-components.es10.js";
+import { AggregateDownloadButton as C, getAvailableFiles as b } from "./ui-components.es17.js";
+import { capitalize as d, Tooltip as N, Stack as x } from "@mui/material";
+import { InfoOutline as v, Check as w } from "@mui/icons-material";
+const k = {
+  field: "ontology",
+  headerName: "Organ/Tissue",
+  type: "singleSelect",
+  valueOptions: ["adipose", "adrenal gland", "blood", "blood vessel", "bone", "bone marrow", "brain", "breast", "connective tissue", "embryo", "epithelium", "esophagus", "eye", "fallopian tube", "gallbladder", "heart", "kidney", "large intestine", "limb", "liver", "lung", "lymphoid tissue", "mouth", "muscle", "nerve", "nose", "ovary", "pancreas", "paraythroid gland", "penis", "placenta", "prostate", "skin", "small intestine", "spinal cord", "spleen", "stomach", "testis", "thymus", "thyroid", "urinary bladder", "uterus", "vagina"],
+  valueFormatter: (e) => e && d(e)
+}, E = {
+  field: "displayname",
+  headerName: "Biosample",
+  valueFormatter: (e) => e && d(e),
+  maxWidth: 300
+}, A = {
+  field: "sampleType",
+  headerName: "Sample Type",
+  type: "singleSelect",
+  valueOptions: ["tissue", "primary cell", "cell line", "in vitro differentiated cells", "organoid"],
+  valueFormatter: (e) => e && d(e)
+}, D = {
+  field: "lifeStage",
+  headerName: "Life Stage",
+  type: "singleSelect",
+  valueOptions: ["adult", "embryonic"],
+  valueFormatter: (e) => e && d(e)
+}, S = {
+  field: "assays",
+  headerName: "Assays",
+  valueGetter: (e, l) => {
+    const s = [];
+    return l.dnase_experiment_accession && s.push("DNase"), l.atac_experiment_accession && s.push("ATAC"), l.h3k4me3_experiment_accession && s.push("H3K4me3"), l.h3k27ac_experiment_accession && s.push("H3K27ac"), l.ctcf_experiment_accession && s.push("CTCF"), s.join(",");
+  },
+  sortComparator: (e, l) => {
+    const s = e.split(",").filter((i) => i.length > 0).length, r = l.split(",").filter((i) => i.length > 0).length;
+    return s - r;
+  },
+  renderCell: (e) => {
+    if (e.rowNode.type === "group") return null;
+    const l = e.row;
+    return /* @__PURE__ */ a.jsx("div", { onClick: (s) => s.stopPropagation(), children: /* @__PURE__ */ a.jsx(h, { row: {
+      dnase: l.dnase_experiment_accession,
+      atac: l.atac_experiment_accession,
+      h3k4me3: l.h3k4me3_experiment_accession,
+      h3k27ac: l.h3k27ac_experiment_accession,
+      ctcf: l.ctcf_experiment_accession
+    } }) });
+  },
+  groupable: !1
+}, _ = ["Core", "Partial", "Ancillary"], n = (e) => !!e && e !== "NA", f = (e) => {
+  const l = {
+    dnase: n(e.dnase_file_accession),
+    h3k4me3: n(e.h3k4me3_file_accession),
+    h3k27ac: n(e.h3k27ac_file_accession),
+    ctcf: n(e.ctcf_file_accession),
+    atac: n(e.atac_file_accession)
+  };
+  if (!Object.values(l).includes(!0)) return null;
+  let s = "Ancillary";
+  return l.dnase && (s = "Partial", l.ctcf && l.h3k4me3 && l.h3k27ac && (s = "Core")), s;
+}, g = [..._, null], H = {
+  field: "collection",
+  headerName: "Collection",
+  type: "singleSelect",
+  valueOptions: [..._],
+  valueGetter: (e, l) => f(l),
+  renderCell: (e) => {
+    const l = e.row;
+    return l.dnase_experiment_accession && !n(l.dnase_file_accession) || l.h3k4me3_experiment_accession && !n(l.h3k4me3_file_accession) || l.h3k27ac_experiment_accession && !n(l.h3k27ac_file_accession) || l.ctcf_experiment_accession && !n(l.ctcf_file_accession) ? /* @__PURE__ */ a.jsx(N, { title: "This sample's H3K4me3 experiment data was not run through the ENCODE pipeline. This assay is ignored when placing this sample in its given collection", children: /* @__PURE__ */ a.jsxs(x, { direction: "row", alignItems: "center", children: [
+      l.name === "GM12866_ENCDO000ABQ" ? "NA" : f(l),
+      /* @__PURE__ */ a.jsx(v, { fontSize: "small" })
+    ] }) }) : f(l);
+  },
+  sortComparator: (e, l) => g.indexOf(e) - g.indexOf(l)
+}, F = {
+  field: "dnase_experiment_accession",
+  headerName: "DNase Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, T = {
+  field: "h3k4me3_experiment_accession",
+  headerName: "H3K4me3 Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, j = {
+  field: "h3k27ac_experiment_accession",
+  headerName: "H3K27ac Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, K = {
+  field: "ctcf_experiment_accession",
+  headerName: "CTCF Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, R = {
+  field: "atac_experiment_accession",
+  headerName: "ATAC Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, $ = {
+  field: "dnase_file_accession",
+  headerName: "DNase File ID",
+  sortable: !1,
+  groupable: !1
+}, O = {
+  field: "h3k4me3_file_accession",
+  headerName: "H3K4me3 File ID",
+  sortable: !1,
+  groupable: !1
+}, Z = {
+  field: "h3k27ac_file_accession",
+  headerName: "H3K27ac File ID",
+  sortable: !1,
+  groupable: !1
+}, I = {
+  field: "ctcf_file_accession",
+  headerName: "CTCF File ID",
+  sortable: !1,
+  groupable: !1
+}, G = {
+  field: "atac_file_accession",
+  headerName: "ATAC File ID",
+  sortable: !1,
+  groupable: !1
+}, B = {
+  field: "dnaseZ",
+  headerName: "DNase Z-scores",
+  valueGetter: (e, l) => l.dnase_experiment_accession && l.dnase_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.dnase_experiment_accession}-${l.dnase_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download DNase z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "DNase", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, U = {
+  field: "h3k4me3Z",
+  headerName: "H3K4me3 Z-scores",
+  valueGetter: (e, l) => (
+    //check if file exists to handle the two samples with unprocessed h3k4me3 experiments: GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA
+    l.h3k4me3_experiment_accession && n(l.h3k4me3_file_accession) ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.h3k4me3_experiment_accession}-${l.h3k4me3_file_accession}.tsv` : null
+  ),
+  renderCell: (e) => {
+    if (["GM12866_ENCDO000ABQ", "neural_crest_cell_ENCDO222AAA"].includes(e.row.name)) return /* @__PURE__ */ a.jsx(o, { disabled: !0, message: () => "This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus z-scores are not available", url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+    if (e.rowNode.type !== "group" && e.value) return /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K4me3 z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+  },
+  groupable: !1,
+  sortable: !1
+}, M = {
+  field: "h3k27acZ",
+  headerName: "H3K27ac Z-scores",
+  valueGetter: (e, l) => l.h3k27ac_experiment_accession && l.h3k27ac_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.h3k27ac_experiment_accession}-${l.h3k27ac_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K27ac z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K27ac", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, z = {
+  field: "ctcfZ",
+  headerName: "CTCF Z-scores",
+  valueGetter: (e, l) => l.ctcf_experiment_accession && l.ctcf_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.ctcf_experiment_accession}-${l.ctcf_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download CTCF z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "CTCF", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, W = {
+  field: "atacZ",
+  headerName: "ATAC Z-scores",
+  valueGetter: (e, l) => l.atac_experiment_accession && l.atac_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.atac_experiment_accession}-${l.atac_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ATAC z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ATAC", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, V = {
+  field: "dnase_signal_url",
+  headerName: "DNase Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download DNase Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "DNase", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, q = {
+  field: "h3k4me3_signal_url",
+  headerName: "H3K4me3 Signal",
+  valueGetter: (e, l) => l.h3k4me3_file_accession === "NA" ? null : e,
+  renderCell: (e) => {
+    if (["GM12866_ENCDO000ABQ", "neural_crest_cell_ENCDO222AAA"].includes(e.row.name)) return /* @__PURE__ */ a.jsx(o, { disabled: !0, message: () => "This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus the signal file is not available", url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+    if (e.rowNode.type !== "group" && e.value) return /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K4me3 Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+  },
+  groupable: !1,
+  sortable: !1
+}, P = {
+  field: "h3k27ac_signal_url",
+  headerName: "H3K27ac Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K27ac Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K27ac", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, Q = {
+  field: "ctcf_signal_url",
+  headerName: "CTCF Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download CTCF Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "CTCF", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, L = {
+  field: "atac_signal_url",
+  headerName: "ATAC Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ATAC Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ATAC", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, J = {
+  field: "chromhmm_url",
+  headerName: "ChromHMM States",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ChromHMM States (.bigBed) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ChromHMM", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, X = {
+  field: "bedurl",
+  headerName: "cCREs (.bed)",
+  align: "center",
+  valueGetter: (e, l, s, r) => {
+    if (u(l)) {
+      const t = y(r, l), c = p(r, t);
+      return c.type === "group" && c.groupingField === "ontology" && typeof c.groupingKey == "string" ? b(c.groupingKey).map((m) => `https://downloads.wenglab.org/${m.filename}`).join(",") : null;
     }
-    p(!0), P(null), L.current = new AbortController();
-    const l = L.current.signal;
-    return f.current = window.setTimeout(() => {
-      (async () => {
-        try {
-          const E = [];
-          await Promise.all(v.map(async (s) => {
-            const x = c.includes("Gene"), k = c.includes("SNP"), F = c.includes("iCRE"), V = c.includes("cCRE"), _ = c.includes("Legacy cCRE"), $ = c.includes("Coordinate"), z = c.includes("Study"), B = c.includes("Ome"), a = [];
-            if (x && !G(s)) {
-              const r = t?.gene ?? 3;
-              a.push(X(s, n, r, u, l).then((o) => o ? se(o, r, typeof u == "object") : []));
-            }
-            if (V && s.toLowerCase().startsWith(n === "GRCh38" ? "eh" : "em")) {
-              const r = t?.ccre ?? 3;
-              a.push(Y(s, n, r, m || !1, l).then((o) => o?.data?.cCREAutocompleteQuery ? re(o.data.cCREAutocompleteQuery, r) : []));
-            }
-            if ($ && G(s) && E.push(...oe(s, n)), _) {
-              const r = t?.legacyCcre ?? 3;
-              a.push(Z(s, n, l).then((o) => o?.data?.ccreMappings ? ce(o.data.ccreMappings, r) : []));
-            }
-            if (n === "GRCh38") {
-              if (F && s.toLowerCase().startsWith("eh")) {
-                const r = t?.icre ?? 3;
-                a.push(D(s, r, l).then((o) => o?.data?.iCREQuery ? ne(o.data.iCREQuery, r) : []));
-              }
-              if (k && s.toLowerCase().startsWith("rs")) {
-                const r = t?.snp ?? 3;
-                a.push(ee(s, n, r, l).then((o) => o?.data?.snpAutocompleteQuery ? ie(o.data.snpAutocompleteQuery, r) : []));
-              }
-              if (z && !G(s) && s !== "") {
-                const r = t?.study ?? 3;
-                a.push(te(s, r, l).then((o) => o?.data?.getGWASStudiesMetadata ? le(o.data.getGWASStudiesMetadata, r) : []));
-              }
-              if (B && !G(s) && s !== "") {
-                const r = t?.ome ?? 3, o = ae.filter((I) => {
-                  const J = s.toLowerCase();
-                  return I.label.toLowerCase().includes(J) || I.keywords?.some((H) => H.toLowerCase().includes(J));
-                }).slice(0, r);
-                a.push(Promise.resolve(ue(o)));
-              }
-            }
-            (await Promise.all(a)).forEach((r) => E.push(...r));
-          })), l.aborted || (W(E), p(!1));
-        } catch (E) {
-          const s = E;
-          l.aborted || (P(s instanceof Error ? s : new Error(String(s))), p(!1));
-        }
-      })();
-    }, C), () => {
-      f.current && (window.clearTimeout(f.current), f.current = null);
-    };
-  }, e[2] = n, e[3] = C, e[4] = u, e[5] = d, e[6] = t?.ccre, e[7] = t?.gene, e[8] = t?.icre, e[9] = t?.legacyCcre, e[10] = t?.ome, e[11] = t?.snp, e[12] = t?.study, e[13] = c, e[14] = m, e[15] = S) : S = e[15];
-  let g;
-  e[16] !== d ? (g = JSON.stringify(d), e[16] = d, e[17] = g) : g = e[17];
-  let y;
-  e[18] !== c ? (y = c.join("|"), e[18] = c, e[19] = y) : y = e[19];
-  let h;
-  e[20] !== t ? (h = JSON.stringify(t), e[20] = t, e[21] = h) : h = e[21];
-  let R;
-  e[22] !== u ? (R = JSON.stringify(u), e[22] = u, e[23] = R) : R = e[23];
-  let b;
-  e[24] !== n || e[25] !== C || e[26] !== m || e[27] !== g || e[28] !== y || e[29] !== h || e[30] !== R ? (b = [g, y, n, h, R, m, C], e[24] = n, e[25] = C, e[26] = m, e[27] = g, e[28] = y, e[29] = h, e[30] = R, e[31] = b) : b = e[31], U(S, b);
-  let q;
-  return e[32] !== A || e[33] !== O || e[34] !== M ? (q = {
-    data: A,
-    loading: M,
-    error: O
-  }, e[32] = A, e[33] = O, e[34] = M, e[35] = q) : q = e[35], q;
-}
-function fe(i) {
-  return !!i && i.trim() !== "";
-}
+    const i = [l.dnase_file_accession, l.h3k4me3_file_accession, l.h3k27ac_file_accession, l.ctcf_file_accession].filter((t) => t != null && t !== "NA");
+    return i.length ? `https://downloads.wenglab.org/Registry-V4/${i.join("_")}.bed` : null;
+  },
+  renderCell: (e) => {
+    if (e.rowNode.type === "group")
+      if (e.rowNode.groupingField === "ontology") {
+        const l = e.rowNode.groupingKey ?? "";
+        return /* @__PURE__ */ a.jsx(C, { ontology: l });
+      } else return null;
+    return /* @__PURE__ */ a.jsx(
+      o,
+      {
+        message: (l) => e.value ? `Download cCREs (.bed) - ${l}` : "cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data",
+        url: e.value,
+        disabled: !e.value,
+        displayName: e.row.displayname,
+        assay: "cCREs",
+        ontology: e.row.ontology
+      }
+    );
+  },
+  groupable: !1,
+  sortable: !1
+}, Y = {
+  field: "bigbedurl",
+  headerName: "cCREs (.bigBed)",
+  align: "center",
+  valueGetter: (e, l) => l.name === "GM12866_ENCDO000ABQ" ? null : l.name === "neural_crest_cell_ENCDO222AAA" ? e.replaceAll("_NA_", "_") : e,
+  renderCell: (e) => e.rowNode.type !== "group" && /* @__PURE__ */ a.jsx(
+    o,
+    {
+      message: (l) => e.value ? `Download cCREs (.bigBed) - ${l}` : "cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data",
+      url: e.value,
+      disabled: !e.value,
+      displayName: e.row.displayname,
+      assay: "cCREs",
+      ontology: e.row.ontology
+    }
+  ),
+  groupable: !1,
+  sortable: !1
+}, ee = {
+  field: "rnaSeq",
+  headerName: "Has RNA Seq",
+  type: "boolean",
+  valueGetter: (e, l) => u(l) ? null : !!l?.rna_seq_tracks?.length,
+  renderCell: (e) => e.value ? /* @__PURE__ */ a.jsx(w, {}) : null
+}, ce = [E, S, k, A, D, H, X, Y, F, $, B, V, R, G, W, L, T, O, U, q, j, Z, M, P, K, I, z, Q, J, ee], de = {
+  displayname: !1,
+  assays: !1,
+  ontology: !1,
+  sampleType: !1,
+  lifeStage: !1,
+  collection: !1,
+  bedurl: !1,
+  bigbedurl: !1,
+  dnase_experiment_accession: !1,
+  dnase_file_accession: !1,
+  dnaseZ: !1,
+  dnase_signal_url: !1,
+  atac_experiment_accession: !1,
+  atac_file_accession: !1,
+  atacZ: !1,
+  atac_signal_url: !1,
+  h3k4me3_experiment_accession: !1,
+  h3k4me3_file_accession: !1,
+  h3k4me3Z: !1,
+  h3k4me3_signal_url: !1,
+  h3k27ac_experiment_accession: !1,
+  h3k27ac_file_accession: !1,
+  h3k27acZ: !1,
+  h3k27ac_signal_url: !1,
+  ctcf_experiment_accession: !1,
+  ctcf_file_accession: !1,
+  ctcfZ: !1,
+  ctcf_signal_url: !1,
+  chromhmm_url: !1,
+  rnaSeq: !1
+};
 export {
-  he as useEntityAutocomplete
+  de as allColsHidden,
+  S as assaysCol,
+  R as atacExpCol,
+  G as atacFileIdCol,
+  L as atacSignalUrlCol,
+  W as atacZscoreUrlCol,
+  X as ccreBedUrlCol,
+  Y as ccreBigBedUrlCol,
+  J as chromHmmUrlCol,
+  H as collectionCol,
+  ce as columns,
+  K as ctcfExpCol,
+  I as ctcfFileIdCol,
+  Q as ctcfSignalUrlCol,
+  z as ctcfZscoreUrlCol,
+  E as displayNameCol,
+  F as dnaseExpCol,
+  $ as dnaseFileIdCol,
+  V as dnaseSignalUrlCol,
+  B as dnaseZscoreUrlCol,
+  j as h3k27acExpCol,
+  Z as h3k27acFileIdCol,
+  P as h3k27acSignalUrlCol,
+  M as h3k27acZscoreUrlCol,
+  T as h3k4me3ExpCol,
+  O as h3k4me3FileIdCol,
+  q as h3k4me3SignalUrlCol,
+  U as h3k4me3ZscoreUrlCol,
+  D as lifeStageCol,
+  k as ontologyCol,
+  ee as rnaSeqCheckCol,
+  A as sampleTypeCol
 };
 //# sourceMappingURL=ui-components.es11.js.map

package/dist/ui-components.es11.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es11.js","sources":["../src/components/GenomeSearch/useEntityAutocomplete.ts"],"sourcesContent":["import { useEffect, useRef, useState } from \"react\";\nimport { getCCREs, getGenes, getICREs, getLegacyCCREs, getSNPs, getStudys } from \"./queries\";\nimport {\n  ccreResultList,\n  geneResultList,\n  getCoordinates,\n  icreResultList,\n  snpResultList,\n  studyResultList,\n  isDomain,\n  legacyCcreResultList,\n  OmesList,\n  omeResultsList,\n} from \"./utils\";\nimport { GenomeSearchProps, Result, ResultType } from \"./types\";\n\ntype Limits = {\n  gene?: number;\n  snp?: number;\n  icre?: number;\n  ccre?: number;\n  legacyCcre?: number;\n  study?: number;\n  ome?: number;\n};\n\ntype HookOptions = {\n  queries: ResultType[];\n  assembly: GenomeSearchProps[\"assembly\"];\n  geneVersion?: GenomeSearchProps[\"geneVersion\"];\n  limits?: Limits;\n  showiCREFlag?: boolean;\n  debounceMs?: number;\n};\n\ntype HookResult = {\n  data: Result[] | null;\n  loading: boolean;\n  error: Error | null;\n};\n\n// Accept either a single string or an array of strings. 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const activeInputs = inputs.filter((i) => !!i && i.trim() !== \"\");\n    if (activeInputs.length === 0) {\n      setData([]);\n      setLoading(false);\n      setError(null);\n      return;\n    }\n\n    setLoading(true);\n    setError(null);\n\n    // Create a new AbortController for this search request\n    abortControllerRef.current = new AbortController();\n    const abortSignal = abortControllerRef.current.signal;\n\n    timeoutRef.current = window.setTimeout(() => {\n      (async () => {\n        try {\n          const aggregated: Result[] = [];\n\n          await Promise.all(\n            activeInputs.map(async (input) => {\n              const qGene = queries.includes(\"Gene\");\n              const qSnp = queries.includes(\"SNP\");\n              const qICRE = queries.includes(\"iCRE\");\n              const qCCRE = queries.includes(\"cCRE\");\n              const qLegacyCcre = queries.includes(\"Legacy cCRE\");\n              const qCoordinate = queries.includes(\"Coordinate\");\n              const qStudy = queries.includes(\"Study\");\n              const qOme = queries.includes(\"Ome\");\n\n              // array for fetch promises (so that we can Promise.all them in parallel)\n              const fetchPromises: Promise<Result[]>[] = [];\n\n              // Genes\n              if (qGene && !isDomain(input)) {\n                const geneLimit = limits?.gene ?? 3;\n                fetchPromises.push(\n                  getGenes(input, assembly, geneLimit, geneVersion, abortSignal).then((geneResults) =>\n                    geneResults ? geneResultList(geneResults as any, geneLimit, typeof geneVersion === \"object\") : []\n                  )\n                );\n              }\n\n              // cCRE - check beginning of input to make sure it matches that assembly\n              if (qCCRE && input.toLowerCase().startsWith(assembly === \"GRCh38\" ? \"eh\" : \"em\")) {\n                const ccreLimit = limits?.ccre ?? 3;\n                fetchPromises.push(\n                  getCCREs(input, assembly, ccreLimit, showiCREFlag || false, abortSignal).then((ccreData) =>\n                    ccreData?.data?.cCREAutocompleteQuery\n                      ? ccreResultList(ccreData.data.cCREAutocompleteQuery, ccreLimit)\n                      : []\n                  )\n                );\n              }\n\n              // Coordinates (synchronous, push directly)\n              if (qCoordinate && isDomain(input)) {\n                aggregated.push(...getCoordinates(input, assembly));\n              }\n\n              if (qLegacyCcre) {\n                const legacyCcreLimit = limits?.legacyCcre ?? 3;\n                fetchPromises.push(\n                  getLegacyCCREs(input, assembly, abortSignal).then((legacyData) =>\n                    legacyData?.data?.ccreMappings\n                      ? legacyCcreResultList(legacyData.data.ccreMappings, legacyCcreLimit)\n                      : []\n                  )\n                );\n              }\n\n              // Human only fetches\n              if (assembly === \"GRCh38\") {\n                if (qICRE && input.toLowerCase().startsWith(\"eh\")) {\n                  const icreLimit = limits?.icre ?? 3;\n                  fetchPromises.push(\n                    getICREs(input, icreLimit, abortSignal).then((icreData) =>\n                      icreData?.data?.iCREQuery ? icreResultList(icreData.data.iCREQuery, icreLimit) : []\n                    )\n                  );\n                }\n\n                if (qSnp && input.toLowerCase().startsWith(\"rs\")) {\n                  const snpLimit = limits?.snp ?? 3;\n                  fetchPromises.push(\n                    getSNPs(input, assembly, snpLimit, abortSignal).then((snpData) =>\n                      snpData?.data?.snpAutocompleteQuery\n                        ? snpResultList(snpData.data.snpAutocompleteQuery, snpLimit)\n                        : []\n                    )\n             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}).slice(0, omeLimit);\n\n                  fetchPromises.push(\n                    Promise.resolve(omeResultsList(filtered))\n                  );\n                }\n              }\n\n              // Execute all parallel fetches and aggregate results\n              const allResults = await Promise.all(fetchPromises);\n              allResults.forEach((results) => aggregated.push(...results));\n            })\n          );\n\n          // Only update state if this request wasn't aborted\n          if (!abortSignal.aborted) {\n            setData(aggregated);\n            setLoading(false);\n          }\n        } catch (err: any) {\n          // Only update error state if this request wasn't aborted\n          if (!abortSignal.aborted) {\n            setError(err instanceof Error ? err : new Error(String(err)));\n            setLoading(false);\n          }\n        }\n      })();\n    }, debounceMs);\n\n    return () => {\n      if (timeoutRef.current) {\n        window.clearTimeout(timeoutRef.current);\n        timeoutRef.current = null;\n      }\n    };\n  }, [JSON.stringify(inputs), queries.join(\"|\"), assembly, JSON.stringify(limits), JSON.stringify(geneVersion), showiCREFlag, debounceMs]);\n\n  return { data, loading, error 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This assay is ignored when placing this sample in its given collection\">\n          <Stack direction={\"row\"} alignItems={\"center\"}>\n            {row.name === \"GM12866_ENCDO000ABQ\" ? \"NA\" : getCollectionForSample(row)}\n            <InfoOutline fontSize=\"small\" />\n          </Stack>\n        </Tooltip>\n      );\n    else return getCollectionForSample(row);\n  },\n  sortComparator: (v1, v2) => sortOrder.indexOf(v1) - sortOrder.indexOf(v2),\n};\n\n//ENCODE Experiment Accession (plain text)\nexport const dnaseExpCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_experiment_accession\",\n  headerName: \"DNase Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3ExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_experiment_accession\",\n  headerName: \"H3K4me3 Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_experiment_accession\",\n  headerName: \"H3K27ac Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfExpCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_experiment_accession\",\n  headerName: \"CTCF Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacExpCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_experiment_accession\",\n  headerName: \"ATAC Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\n\n//ENCODE File ID (plain text)\nexport const dnaseFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_file_accession\",\n  headerName: \"DNase File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3FileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_file_accession\",\n  headerName: \"H3K4me3 File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_file_accession\",\n  headerName: \"H3K27ac File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_file_accession\",\n  headerName: \"CTCF File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_file_accession\",\n  headerName: \"ATAC File ID\",\n  sortable: false,\n  groupable: false,\n};\n\nexport const dnaseZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnaseZ\",\n  headerName: \"DNase Z-scores\",\n  valueGetter: (_, row) =>\n    row.dnase_experiment_accession && row.dnase_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.dnase_experiment_accession}-${row.dnase_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3ZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3Z\",\n  headerName: \"H3K4me3 Z-scores\",\n  valueGetter: (_, row) =>\n    //check if file exists to handle the two samples with unprocessed h3k4me3 experiments: GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA\n    row.h3k4me3_experiment_accession && fileExists(row.h3k4me3_file_accession)\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k4me3_experiment_accession}-${row.h3k4me3_file_accession}.tsv`\n      : null,\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus z-scores are not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 z-score by cCRE (.tsv) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27acZ\",\n  headerName: \"H3K27ac Z-scores\",\n  valueGetter: (_, row) =>\n    row.h3k27ac_experiment_accession && row.h3k27ac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k27ac_experiment_accession}-${row.h3k27ac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcfZ\",\n  headerName: \"CTCF Z-scores\",\n  valueGetter: (_, row) =>\n    row.ctcf_experiment_accession && row.ctcf_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.ctcf_experiment_accession}-${row.ctcf_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atacZ\",\n  headerName: \"ATAC Z-scores\",\n  valueGetter: (_, row) =>\n    row.atac_experiment_accession && row.atac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.atac_experiment_accession}-${row.atac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const dnaseSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_signal_url\",\n  headerName: \"DNase Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3SignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_signal_url\",\n  headerName: \"H3K4me3 Signal\",\n  valueGetter: (value, row) => (row.h3k4me3_file_accession === \"NA\" ? null : value),\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus the signal file is not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 Signal (.bigWig) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_signal_url\",\n  headerName: \"H3K27ac Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_signal_url\",\n  headerName: \"CTCF Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_signal_url\",\n  headerName: \"ATAC Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const chromHmmUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"chromhmm_url\",\n  headerName: \"ChromHMM States\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ChromHMM States (.bigBed) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ChromHMM\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bedurl\",\n  headerName: \"cCREs (.bed)\",\n  align: \"center\",\n  valueGetter: (_, row, __, apiRef) => {\n    if (isAutogeneratedRow(row)) {\n      const id = gridRowIdSelector(apiRef, row);\n      const rowNode = gridRowNodeSelector(apiRef, id);\n      const isGroupingByOntology = rowNode.type === \"group\" && rowNode.groupingField === \"ontology\";\n      if (isGroupingByOntology && typeof rowNode.groupingKey === \"string\") {\n        return getAvailableFiles(rowNode.groupingKey)\n          .map((x) => `https://downloads.wenglab.org/${x.filename}`)\n          .join(\",\");\n      } else return null;\n    }\n    const signalIDs = [\n      row.dnase_file_accession,\n      row.h3k4me3_file_accession,\n      row.h3k27ac_file_accession,\n      row.ctcf_file_accession,\n    ].filter((id) => id !== null && id !== undefined && id !== \"NA\");\n    if (!signalIDs.length) return null // aka is ATAC-only\n    return `https://downloads.wenglab.org/Registry-V4/${signalIDs.join(\"_\")}.bed`;\n  },\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.rowNode.groupingField === \"ontology\") {\n        const ontology = (params.rowNode.groupingKey as string) ?? \"\";\n        return <AggregateDownloadButton ontology={ontology} />;\n      } else return null;\n    }\n    return (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBigBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bigbedurl\",\n  headerName: \"cCREs (.bigBed)\",\n  align: 'center',\n  valueGetter: (value: string, row) => {\n    if (row.name === \"GM12866_ENCDO000ABQ\") return null //This sample has no cCREs file\n    if (row.name === \"neural_crest_cell_ENCDO222AAA\") return value.replaceAll('_NA_', '_') //The url in file includes \"NA\" H3K4me3 file ID\n    else return value\n  },\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" && (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bigBed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const rnaSeqCheckCol: GridColDef<EncodeBiosample> = {\n  field: \"rnaSeq\",\n  headerName: \"Has RNA Seq\",\n  type: \"boolean\",\n  valueGetter: (_, row) => (isAutogeneratedRow(row) ? null : !!row?.rna_seq_tracks?.length),\n  renderCell: (params) => {\n    if (params.value) {\n      return <Check />;\n    } else return null;\n  },\n};\n\nexport const columns: GridColDef<EncodeBiosample>[] = [\n  displayNameCol,\n  assaysCol,\n  ontologyCol,\n  sampleTypeCol,\n  lifeStageCol,\n  collectionCol,\n  ccreBedUrlCol,\n  ccreBigBedUrlCol,\n  dnaseExpCol,\n  dnaseFileIdCol,\n  dnaseZscoreUrlCol,\n  dnaseSignalUrlCol,\n  atacExpCol,\n  atacFileIdCol,\n  atacZscoreUrlCol,\n  atacSignalUrlCol,\n  h3k4me3ExpCol,\n  h3k4me3FileIdCol,\n  h3k4me3ZscoreUrlCol,\n  h3k4me3SignalUrlCol,\n  h3k27acExpCol,\n  h3k27acFileIdCol,\n  h3k27acZscoreUrlCol,\n  h3k27acSignalUrlCol,\n  ctcfExpCol,\n  ctcfFileIdCol,\n  ctcfZscoreUrlCol,\n  ctcfSignalUrlCol,\n  chromHmmUrlCol,\n  rnaSeqCheckCol,\n];\n\n/**\n * useful for resetting visible columns by spreading this then overriding with visible cols\n */\nexport const allColsHidden = {\n  displayname: false,\n  assays: false,\n  ontology: false,\n  sampleType: false,\n  lifeStage: false,\n  collection: false,\n  bedurl: false,\n  bigbedurl: false,\n  dnase_experiment_accession: false,\n  dnase_file_accession: false,\n  dnaseZ: false,\n  dnase_signal_url: false,\n  atac_experiment_accession: false,\n  atac_file_accession: false,\n  atacZ: false,\n  atac_signal_url: false,\n  h3k4me3_experiment_accession: false,\n  h3k4me3_file_accession: false,\n  h3k4me3Z: false,\n  h3k4me3_signal_url: false,\n  h3k27ac_experiment_accession: 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